rs1748019

Variant names:

• chr1-17342481-G-C
• rs1748019
• NM_012387.3:c.935+79G>C

Your query was ambiguous. Multiple possible variants found:

• chr1-17342481-G-C
• chr1-17342481-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_012387.3(PADI4):​c.935+79G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0901 in 850,980 control chromosomes in the GnomAD database, including 3,807 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.098 (784 hom., cov: 32)
  • Exomes 𝑓: 0.088 (3023 hom.)
• Consequence: PADI4 NM_012387.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19

Genes affected

PADI4 (HGNC:18368): (peptidyl arginine deiminase 4) This gene is a member of a gene family which encodes enzymes responsible for the conversion of arginine residues to citrulline residues. This gene may play a role in granulocyte and macrophage development leading to inflammation and immune response. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PADI4	NM_012387.3	c.935+79G>C		intron_variant	Intron 8 of 15	ENST00000375448.4	NP_036519.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PADI4	ENST00000375448.4	c.935+79G>C		intron_variant	Intron 8 of 15	1	NM_012387.3	ENSP00000364597.4

Frequencies

GnomAD3 genomes AF: 0.0975 AC: 14810 AN: 151938 Hom.: 777 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.0562

Gnomad ASJ AF: 0.0588

Gnomad EAS AF: 0.0491

Gnomad SAS AF: 0.0483

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0973

Gnomad OTH AF: 0.0845

GnomAD4 exome AF: 0.0884 AC: 61804 AN: 698922 Hom.: 3023 AF XY: 0.0863 AC XY: 31156 AN XY: 360912

Gnomad4 AFR exome AF: 0.121

Gnomad4 AMR exome AF: 0.0358

Gnomad4 ASJ exome AF: 0.0608

Gnomad4 EAS exome AF: 0.0494

Gnomad4 SAS exome AF: 0.0460

Gnomad4 FIN exome AF: 0.109

Gnomad4 NFE exome AF: 0.0980

Gnomad4 OTH exome AF: 0.0892

GnomAD4 genome AF: 0.0975 AC: 14831 AN: 152058 Hom.: 784 Cov.: 32 AF XY: 0.0968 AC XY: 7197 AN XY: 74340

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.0559

Gnomad4 ASJ AF: 0.0588

Gnomad4 EAS AF: 0.0490

Gnomad4 SAS AF: 0.0483

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.0973

Gnomad4 OTH AF: 0.0836

Alfa AF: 0.0557 Hom.: 49

Bravo AF: 0.0935

Asia WGS AF: 0.0830 AC: 288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.3
DANN	Benign	0.53

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1748019; hg19: chr1-17668976;